I've used a number of different *nix-based systems of the years, and it seems like every flavor of Bash I use has a different algorithm for deciding which startup scripts to run. For the purposes of tasks like setting up environment variables and aliases and printing startup messages (e.g. MOTDs), which startup script is the appropriate place to do these?

What's the difference between putting things in .bashrc, .bash_profile, and .environment? I've also seen other files such as .login, .bash_login, and .profile; are these ever relevant? What are the differences in which ones get run when logging in physically, logging in remotely via ssh, and opening a new terminal window? Are there any significant differences across platforms (including Mac OS X (and its Terminal.app) and Cygwin Bash)?

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7 Answers
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The main difference with shell config files is that some are only read by "login" shells (eg. when you login from another host, or login at the text console of a local unix machine). these are the ones called, say, .login or .profile or .zlogin (depending on which shell you're using).

Then you have config files that are read by "interactive" shells (as in, ones connected to a terminal (or pseudo-terminal in the case of, say, a terminal emulator running under a windowing system). these are the ones with names like .bashrc, .tcshrc, .zshrc, etc.

bash complicates this in that .bashrc is only read by a shell that's both interactive and non-login, so you'll find most people end up telling their .bash_profile to also read .bashrc with something like

[[ -r ~/.bashrc ]] && . ~/.bashrc

Other shells behave differently - eg with zsh, .zshrc is always read for an interactive shell, whether it's a login one or not.

The manual page for bash explains the circumstances under which each file is read. Yes, behaviour is generally consistent between machines.

.profile is simply the login script filename originally used by /bin/sh. bash, being generally backwards-compatible with /bin/sh, will read .profile if one exists.

Login shells are the ones that are read one you login (so, they are not executed when merely starting up xterm, for example). There are other ways to login. For example using an X display manager. Those have other ways to read and export environment variables at login time.

Also read the INVOCATION chapter in the manual. It says "The following paragraphs describe how bash executes its startup files.", i think that's a spot-on :) It explains what an "interactive" shell is too.

Bash does not know about .environment. I suspect that's a file of your distribution, to set environment variables independent of the shell that you drive.

I found information about .bashrc and .bash_profile here to sum it up:

.bash_profile is executed when you
login. Stuff you put in there might be
your PATH and other important
environment variables.

.bashrc is used for non login shells.
I'm not sure what that means. I know
that RedHat
executes it everytime you start
another shell (su to this user or
simply calling bash again) You might
want to put aliases in there but again
I am not sure what that means. I
simply ignore it myself.

.profile is the equivalent of
.bash_profile for the root. I think
the name is changed to let other
shells (csh, sh, tcsh) use it as well.
(you don't need one as a user)

There is also .bash_logout wich
executes at, yeah good guess...logout.
You might want to stop deamons or even
make a little housekeeping . You can
also add "clear" there if you want to
clear the screen when you log out.

Also there is a complete follow up on each of the configurations files here

These are probably even distro.-dependant, not all distros choose to have each configuraton with them and some have even more. But when they have the same name, they usualy include the same content.

According to Josh Staiger, Mac OS X's Terminal.app actually runs a login shell rather than a non-login shell by default for each new terminal window, calling .bash_profile instead of .bashrc.

He recommends:

Most of the time you don’t want to maintain two separate config files
for login and non-login shells — when you set a PATH, you want it to
apply to both. You can fix this by sourcing .bashrc from your
.bash_profile file, then putting PATH and common settings in .bashrc.

To do this, add the following lines to .bash_profile:

if [ -f ~/.bashrc ]; then
source ~/.bashrc
fi

Now when you login to your
machine from a console .bashrc will be called.